Skip to content

remove plotting abs as the defauls for plotting volumetric - #13989

Merged
larsoner merged 5 commits into
mne-tools:mainfrom
ualsbombe:issue_13983_glass_brain_signed
Sep 10, 2026
Merged

remove plotting abs as the defauls for plotting volumetric#13989
larsoner merged 5 commits into
mne-tools:mainfrom
ualsbombe:issue_13983_glass_brain_signed

Conversation

@ualsbombe

@ualsbombe ualsbombe commented Jun 26, 2026

Copy link
Copy Markdown
Contributor

Reference issue (if any)

What does this implement/fix?

Makes sure that the default is not to plot abs for glass brain - it changes plot_abs to False

Additional information

@welcome

welcome Bot commented Jun 26, 2026

Copy link
Copy Markdown

Hello! 👋 Thanks for opening your first pull request here! ❤️ We will try to get back to you soon. 🚴

larsoner
larsoner reviewed Jun 29, 2026
View reviewed changes

@larsoner larsoner left a comment

Copy link
Copy Markdown
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Arguably a bugfix... so needs a doc/changes/dev/13989.bugfix.rst that mentions that two-sided data will now be plotted properly in glass-brain mode

Comment thread mne/source_estimate.py Outdated
initial_time=None,
initial_pos=None,
verbose=None,
plot_abs=False,

@larsoner larsoner Jun 29, 2026

Copy link
Copy Markdown
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks like cruft from an earlier implementation?

Suggested change
plot_abs=False,

@larsoner

larsoner commented Sep 10, 2026

Copy link
Copy Markdown
Member

@ualsbombe do you have time to come back to this? If not, I could push commits to finish probably

@ualsbombe

ualsbombe commented Sep 10, 2026

Copy link
Copy Markdown
Contributor Author

Not at this moment, sorry - I would very much appreciate you finishing it. To be honest, I haven't been pushing to MNE-Python, and it's changed a bit since I tried last. But also full understanding if you do not have the time now.

@larsoner
FIX: More
e12369d
@larsoner
Merge remote-tracking branch 'upstream/main' into issue_13983_glass_b…
c66f29a 
…rain_signed

* upstream/main: (251 commits)
  Coregistration GUI modernisation (phase 4) (mne-tools#14285)
  Dipole GUI interactivity and visual enhancements (phase 2) (mne-tools#14291)
  Width [circle deploy] [skip azp] [skip actions]
  Post-release deprecations (mne-tools#14290)
  FIX: Come on [circle deploy] [skip azp] [skip actions]
  PyVista try again [circle deploy] [skip azp] [skip actions]
  FIX: PyVista [circle deploy] [skip azp] [skip actions]
  FIX: Really [circle deploy] [skip azp] [skip actions]
  FIX: Doc
  Release commit [circle deploy]
  MAINT: Update code credit (mne-tools#14289)
  MAINT: Update pre-commit hook versions (mne-tools#14288)
  BUG: use fixed normalized CTPS cutoff for automatic ECG detection (mne-tools#14279)
  Move toward docstacks [circle deploy] [skip azp] [skip actions]
  Fix tfce (mne-tools#14286)
  FIX: Improve channel name rendering in `plot_alignment` (mne-tools#13773)
  Don't shift placeholder proc_history dates in anonymize_info (mne-tools#14248)
  MRG: Avoid pytest 10 warnings in sklearn estimator checks (mne-tools#14283)
  MAINT: Update pre-commit hook versions (mne-tools#14282)
  DOC: Add osl-dynamics to related software list (mne-tools#14268)
  ...
@larsoner larsoner added the backport-candidate on-merge: backport to maint/1.13 label Sep 10, 2026
@larsoner
larsoner enabled auto-merge (squash) September 10, 2026 14:28
@larsoner

larsoner commented Sep 10, 2026

Copy link
Copy Markdown
Member

Okay marking for merge-when-green, thanks in advance @ualsbombe !

@larsoner
larsoner merged commit 028207b into mne-tools:main Sep 10, 2026
26 checks passed
@meeseeksmachine meeseeksmachine mentioned this pull request Sep 10, 2026
Merged
larsoner pushed a commit that referenced this pull request Sep 10, 2026
@meeseeksmachine @ualsbombe
Backport PR #13989 on branch maint/1.13 (remove plotting abs as the d…
0b9e60c 
…efauls for plotting volumetric) (#14294)

Co-authored-by: Lau Møller Andersen <ualsbombe@protonmail.com>
larsoner added a commit to drammock/mne-python that referenced this pull request Sep 11, 2026
@larsoner
Merge remote-tracking branch 'upstream/main' into edf
95f04e2 
* upstream/main: (75 commits)
  Brain GUI modernization (Phase 7) (mne-tools#14270)
  Fix bug with SciPy 1.18.0 EEGLAB reading (mne-tools#14293)
  remove plotting abs as the defauls for plotting volumetric (mne-tools#13989)
  Coregistration GUI modernisation (phase 4) (mne-tools#14285)
  Dipole GUI interactivity and visual enhancements (phase 2) (mne-tools#14291)
  Width [circle deploy] [skip azp] [skip actions]
  Post-release deprecations (mne-tools#14290)
  FIX: Come on [circle deploy] [skip azp] [skip actions]
  PyVista try again [circle deploy] [skip azp] [skip actions]
  FIX: PyVista [circle deploy] [skip azp] [skip actions]
  FIX: Really [circle deploy] [skip azp] [skip actions]
  FIX: Doc
  Release commit [circle deploy]
  MAINT: Update code credit (mne-tools#14289)
  MAINT: Update pre-commit hook versions (mne-tools#14288)
  BUG: use fixed normalized CTPS cutoff for automatic ECG detection (mne-tools#14279)
  Move toward docstacks [circle deploy] [skip azp] [skip actions]
  Fix tfce (mne-tools#14286)
  FIX: Improve channel name rendering in `plot_alignment` (mne-tools#13773)
  Don't shift placeholder proc_history dates in anonymize_info (mne-tools#14248)
  ...

# Conflicts:
#	mne/io/edf/tests/test_edf.py
larsoner added a commit to natinew77-creator/mne-python that referenced this pull request Sep 11, 2026
@larsoner
Merge remote-tracking branch 'upstream/main' into lite-setup-cell
1a1da29 
* upstream/main: (22 commits)
  fix EDF round-trip (mne-tools#14296)
  Brain GUI modernization (Phase 7) (mne-tools#14270)
  Fix bug with SciPy 1.18.0 EEGLAB reading (mne-tools#14293)
  remove plotting abs as the defauls for plotting volumetric (mne-tools#13989)
  Coregistration GUI modernisation (phase 4) (mne-tools#14285)
  Dipole GUI interactivity and visual enhancements (phase 2) (mne-tools#14291)
  Width [circle deploy] [skip azp] [skip actions]
  Post-release deprecations (mne-tools#14290)
  FIX: Come on [circle deploy] [skip azp] [skip actions]
  PyVista try again [circle deploy] [skip azp] [skip actions]
  FIX: PyVista [circle deploy] [skip azp] [skip actions]
  FIX: Really [circle deploy] [skip azp] [skip actions]
  FIX: Doc
  Release commit [circle deploy]
  MAINT: Update code credit (mne-tools#14289)
  MAINT: Update pre-commit hook versions (mne-tools#14288)
  BUG: use fixed normalized CTPS cutoff for automatic ECG detection (mne-tools#14279)
  Move toward docstacks [circle deploy] [skip azp] [skip actions]
  Fix tfce (mne-tools#14286)
  FIX: Improve channel name rendering in `plot_alignment` (mne-tools#13773)
  ...

# Conflicts:
#	mne/viz/backends/tests/test_renderer.py
larsoner added a commit to natinew77-creator/mne-python that referenced this pull request Sep 11, 2026
@larsoner
Merge remote-tracking branch 'upstream/main' into lite-docs-wiring
7561f0a 
* upstream/main: (25 commits)
  ENH: add the JupyterLite notebook setup cell (JupyterLite split 4/5) (mne-tools#14150)
  FIX: Ver [circle deploy] [skip azp] [skip actions]
  Hotfix
  fix EDF round-trip (mne-tools#14296)
  Brain GUI modernization (Phase 7) (mne-tools#14270)
  Fix bug with SciPy 1.18.0 EEGLAB reading (mne-tools#14293)
  remove plotting abs as the defauls for plotting volumetric (mne-tools#13989)
  Coregistration GUI modernisation (phase 4) (mne-tools#14285)
  Dipole GUI interactivity and visual enhancements (phase 2) (mne-tools#14291)
  Width [circle deploy] [skip azp] [skip actions]
  Post-release deprecations (mne-tools#14290)
  FIX: Come on [circle deploy] [skip azp] [skip actions]
  PyVista try again [circle deploy] [skip azp] [skip actions]
  FIX: PyVista [circle deploy] [skip azp] [skip actions]
  FIX: Really [circle deploy] [skip azp] [skip actions]
  FIX: Doc
  Release commit [circle deploy]
  MAINT: Update code credit (mne-tools#14289)
  MAINT: Update pre-commit hook versions (mne-tools#14288)
  BUG: use fixed normalized CTPS cutoff for automatic ECG detection (mne-tools#14279)
  ...
larsoner added a commit to wmvanvliet/mne-python that referenced this pull request Sep 16, 2026
@larsoner
Merge commit '0311e444b0450ce9d2b2b304cebe7d5343533357' into info-hea…
913fefb 
…d-sphere

* commit '0311e444b0450ce9d2b2b304cebe7d5343533357':
  Fix static doc viewing in IDEs (mne-tools#14195)
  Fix COLA for odd sizes (mne-tools#14312)
  add type hints to mne/_fiff/ module (mne-tools#14278)
  ENH: wire the JupyterLite build into the docs (JupyterLite split 5/5) (mne-tools#14157)
  MAINT: Update pre-commit hook versions (mne-tools#14306)
  Small documentation fix for "Frequency and time-frequency sensor analysis" tutorial (mne-tools#14304)
  FIX: don't mutate cached ICA sources in plot_sources properties (mne-tools#14303)
  Fix bug with lite backend closing (mne-tools#14302)
  Fix for NumPy eig change [circle deploy] (mne-tools#14300)
  No PyQt5 [circle deploy] [skip azp] [skip actions]
  ENH: add the JupyterLite notebook setup cell (JupyterLite split 4/5) (mne-tools#14150)
  FIX: Ver [circle deploy] [skip azp] [skip actions]
  Hotfix
  fix EDF round-trip (mne-tools#14296)
  Brain GUI modernization (Phase 7) (mne-tools#14270)
  Fix bug with SciPy 1.18.0 EEGLAB reading (mne-tools#14293)
  remove plotting abs as the defauls for plotting volumetric (mne-tools#13989)
  Coregistration GUI modernisation (phase 4) (mne-tools#14285)
  Dipole GUI interactivity and visual enhancements (phase 2) (mne-tools#14291)
larsoner added a commit to CarinaFo/mne-python that referenced this pull request Sep 16, 2026
@larsoner
Merge remote-tracking branch 'upstream/main' into cluster-api-review
8c21321 
* upstream/main: (91 commits)
  Fix static doc viewing in IDEs (mne-tools#14195)
  Fix COLA for odd sizes (mne-tools#14312)
  add type hints to mne/_fiff/ module (mne-tools#14278)
  ENH: wire the JupyterLite build into the docs (JupyterLite split 5/5) (mne-tools#14157)
  MAINT: Update pre-commit hook versions (mne-tools#14306)
  Small documentation fix for "Frequency and time-frequency sensor analysis" tutorial (mne-tools#14304)
  FIX: don't mutate cached ICA sources in plot_sources properties (mne-tools#14303)
  Fix bug with lite backend closing (mne-tools#14302)
  Fix for NumPy eig change [circle deploy] (mne-tools#14300)
  No PyQt5 [circle deploy] [skip azp] [skip actions]
  ENH: add the JupyterLite notebook setup cell (JupyterLite split 4/5) (mne-tools#14150)
  FIX: Ver [circle deploy] [skip azp] [skip actions]
  Hotfix
  fix EDF round-trip (mne-tools#14296)
  Brain GUI modernization (Phase 7) (mne-tools#14270)
  Fix bug with SciPy 1.18.0 EEGLAB reading (mne-tools#14293)
  remove plotting abs as the defauls for plotting volumetric (mne-tools#13989)
  Coregistration GUI modernisation (phase 4) (mne-tools#14285)
  Dipole GUI interactivity and visual enhancements (phase 2) (mne-tools#14291)
  Width [circle deploy] [skip azp] [skip actions]
  ...
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@larsoner larsoner larsoner left review comments
@drammock drammock Awaiting requested review from drammock drammock is a code owner
@agramfort agramfort Awaiting requested review from agramfort agramfort is a code owner

Assignees

No one assigned

Labels

backport-candidate on-merge: backport to maint/1.13

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

2 participants

@ualsbombe @larsoner